You were right!
Bioperl-1.5.1 is working perfectly with blast.
Thanks very much for all the help everybody, It was very nice of you :-).
Anders.
>>>Jason Stajich <jason.stajich at duke.edu> 12/21/05 4:09 pm >>>
Make sure you are using the latest version of bioperl - NCBI changed
the interface and we now have Bio::SearchIO as the default parser.
It works fine for me on bioperl 1.5.1
#23 shouldn't have to work as root, but I haven't been following the
thread so I don't know what you are changing.
On Dec 21, 2005, at 10:02 AM, Anders Stegmann wrote:
>Michael,
>>It worked as root!!!
>>the blaststandalone bptutorial 23 is working!
>>great job.
>>BUT bptutorial 22 is still not working. still getting
>>Beginning run_remoteblast example...
>submitted Blast job
>retrieving results...
>>-------------------- WARNING ---------------------
>MSG: Possible error (1) while parsing BLAST report!
>---------------------------------------------------
>Use of uninitialized value in substitution (s///) at Bio/Tools/
>BPlite.pm line 337, <GEN3> line 29.
>Use of uninitialized value in substitution (s///) at Bio/Tools/
>BPlite.pm line 338, <GEN3> line 29.
>Use of uninitialized value in substitution (s///) at Bio/Tools/
>BPlite.pm line 339, <GEN3> line 29.
>Use of uninitialized value in patt
>>any suggestions?
>>Anders.
>>>>>>>michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> 12/21/05
>>>>3:01 pm >>>
>Dude
>>Try
>>find / -name ecoli.nt.nin
>>This will give you the location of your blast data directory. For an
>example, mine is in /usr/local/blast/data/ecoli.nt.nin
>>Now
>>export PATH=$PATH:/usr/local/blast/bin
>export BLASTDB=/usr/local/blast/data/ # get this from the find command
>above
>export BLASTMAT=/usr/local/blast/data/ # get this from the find
>command above
>>perl -w bptutorial.pl 23
>>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org>[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Anders
>Stegmann
>Sent: 21 December 2005 13:41
>To: bioperl-l at bioperl.org>Subject: [Bioperl-l] Blast doesn't work
>>Torsten,
>>SUSE 10.0 is the brand new version the linux SUSE OS.
>>writing: export PATH=/usr/local/blast/bin:$PATH./bptutorial 23
>>gives me:
>>bash: export
>PATH=/usr/local/blast/bin:/home/anst/bin:/usr/local/bin:/usr/bin:/
>usr/X1
>1R6/bin:/bin:/home/anst/blast/bin:/usr/games:/opt/gnome/bin:/opt/
>kde3/bi
>n:/usr/lib/mit/bin:/usr/lib/mit/sbin./bptutorial 23: No such file or
>directory
>>Yes! there is definitely a file called blastall in the
>/usr/local/blast/bin directory and it works if I use it
>independently of
>bioperl.
>>The thing is that I have never before needed/used to download the ncbi
>blast program independently.
>Shouldn't it be enough to install the Bundle?
>>Also, when writing
>>perl -w bptutorial.pl 23
>>I get:
>>Beginning run_standaloneblast example...
>[blastall] WARNING: Test1: Unable to open ecoli.nt.nin
>>------------- EXCEPTION -------------
>MSG: blastall call crashed: 256 /usr/local/blast/bin/blastall -p
>blastn
>-d /usr/local/blast/bin/data/ecoli.nt -i /tmp/zM1t9HD2jq -o
>/tmp/FCGPZQlclD
>>STACK Bio::Tools::Run::StandAloneBlast::_runblast
>Bio/Tools/Run/StandAloneBlast.pm:732
>STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
>Bio/Tools/Run/StandAloneBlast.pm:680
>STACK Bio::Tools::Run::StandAloneBlast::blastall
>Bio/Tools/Run/StandAloneBlast.pm:536
>STACK main::__ANON__ bptutorial.pl:3279 STACK main::run_examples
>bptutorial.pl:4156 STACK toplevel bptutorial.pl:4245
>>Notice in line 2: Unable to open ecoli.nt.nin. This is a remnant
>from an
>E.coli. database formatation I did much earlier and independently of
>bioperl.
>Thus, the ncbi standaloneblast program works, but not with bioperl!
>>Why does bioperl fetch an unrelated file in the /usr/local/blast/data
>directory?
>Is like it is trying to run something it shouldn't.
>>Anders.
>>>>Torsten Seemann <torsten.seemann at infotech.monash.edu.au> 12/21/05
>12:50 pm >>> >I have tried >export BLASTDIR=/usr/local/blast/bin
>(where my blastall binary is) >I get the same? (I assume you are on
>Unix, not Windows) Does it work when you do this? export
>PATH=/usr/local/blast/bin:$PATH ./bptutorial 23 Is there definitely a
>file called 'blastall' in /usr/local/blast/bin which is EXECUTABLE and
>READABLE by the user running the tutorial? -- Torsten Seemann
>Victorian
>Bioinformatics Consortium, Monash University, Australia
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12